Complete chloroplast genome of Exochorda serratifolia (Rosaceae)

Abstract Exochorda serratifolia (pearlbush) is a rosid shrub found in northeast Asia, including the Korean peninsula. This ornamental plant has white inflorescences and strong insect resistance; however, its genetic diversity is poorly understood and a complete plastid genome is unavailable. Here, we determined the complete chloroplast genome of E. serratifolia through de novo assembly using next-generation sequencing. The E. serratifolia chloroplast genome was 160,558 bp, comprising a large single-copy (LSC) region of 88,514 bp, a small single-copy (SSC) region of 19,308 bp, and two inverted repeat regions (IRs) of 26,368 bp each. We annotated 112 genes: 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. This reference plastid genome increases our understanding of the phylogenetic relationships of E. serratifolia among Rosaceae plants.

Exochorda serratifolia S. Moore 1877 is a deciduous shrub distributed in northeast Asia, including Liaoning (Qian mountains) in China (Cuizhi and Alexander 2003). It occurs sporadically on the Korean peninsula (Kim et al. 2014). This ornamental shrub has white inflorescences and possesses shade tolerance, freezing tolerance, and insect resistance (Lee et al. 1987). The species is an important genetic resource in Korea, being designated as a biological resource subject to approval for export abroad by the Korean Government. Despite the important economic value of E. serratifolia as a genetic resource, studies on its genetic diversity and cultivar identification are very limited. Phenotypic variation among habitats (Song et al. 2016) and ISSR variation among populations (Hong et al. 2013) have been investigated, but not fully resolved. Partial plastid genomic information for this species is available (Zhang et al. 2017); however, characterizing the complete chloroplast genome as a reference is necessary.
Leaf samples were collected from the native habitat in Cheongju, Korea (36 39 0 03.9 00 N, 127 31 0 16.4 00 E), which is designated and protected as a Forest Genetic Resource Reserve (FGRR). A dried voucher specimen was deposited in the Herbarium of the National Institute of Horticulture and Herbal Science, Eumsung, South Korea (IN; http://www.nihhs. go.kr/; voucher number: MPS006522-1; contact: Yoongee Lee, yoong0625@korea.kr). Genomic DNA was extracted using a DNeasy Plant Mini kit (Qiagen, Valencia, CA). A genomic library was constructed using the Illumina HiSeq platform. Raw data obtained through next-generation sequencing were trimmed using the CLC quality trim program (ver. 4.21) in the CLC Assembly Cell package (version 4.2.1, https://www.qiagenbioinformatics.com/products/clc-assembly-cell/), and the chloroplast genome contig was secured and its structure determined through de novo assembly. Loci were annotated using the GeSeq program (https://chlorobox.mpimp-golm. mpg.de/geseq-app.html) (Tillich et al. 2017), with manual curation based on BLAST search for final review. The complete chloroplast genome sequence of E. serratifolia was deposited in GenBank under accession no. MZ981786.
The complete E. serratifolia chloroplast genome was 160,558 bp in length with GC content of 36.5%. The circular structure consisted of a large single-copy (LSC) region of 88,514 bp, a small single-copy (SSC) region of 19,308 bp, and two inverted repeat regions (IRs) of 26,368 bp each. We annotated 112 genes, representing 78 protein-coding genes, 30 tRNA genes, and four rRNA genes.

Author contributions
S.K., J.L., and Y.L. conceived and designed the study. S.K., E.Y., J.H.P., and J.L. analyzed the data. N.J. and S.K. performed the experiments. N.J., J.L., and Y.L. wrote the manuscript. All authors read and approved the final manuscript.

Ethical approval
Exochorda serratifolia samples were collected by Serim Kim, a researcher of Memoreal Co., Ltd., with permission from Jinsoon Oh, the Hwajangsa Temple Governor who is responsible for the Forest Genetic Resource Reserve. The plant is freely accessible to Serim Kim with noncommercial resource purpose. The authors comply with relevant institutional, national, and international guidelines and legislation for plant study.

Disclosure statement
No potential conflict of interest was reported by the authors.